The goal of Non-Rigid Structure from Motion (NRSfM) is to recover 3D shapes of a deformable object from a monocular video sequence. Procrustean Normal Distribution (PND) is one of the best algorithms for NRSfM. It uses Generalized Procrustes Analysis (GPA) model to accomplish this task. But the biggest problem of this method is that just a few non-rigid points in 2D observations can largely affect the reconstruction performance. We believe that PND can achieve better reconstruction performance by eliminating the affection of these points. In this paper, we present a novel reconstruction method to solve this problem. We present two solutions to simply classify the points into non-rigid and nearly rigid points. After that, we use EM algorithm of PND to recover 3D structure again for nearly rigid points. Experimental results show that the proposed method outperforms the existing state-of-the-art algorithms.